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Chapter 2. the Beginnings of Genomic Biology – Classical Genetics Contents Chapter 2. The beginnings of Genomic Biology – Classical Genetics Contents 2. The beginnings of Genomic Biology – classical genetics 2.1. Mendel & Darwin – traits are conditioned by genes CHAPTER 2. THE BEGINNINGS OF GENOMIC 2.2. Genes are carried on chromosomes 2.3. The chromosomal theory of inheritance BIOLOGY –CLASSICAL GENETICS 2.4. Additional Complexity of Mendelian Inheritance 2.4.1. Multiple alleles 2.4.2. Incomplete dominance and co-dominance 2.4.3. Sex linked inheritance 2.4.4. Epistasis It should be clear that the beginings of genomic 2.4.5. Epigenetics 2.5. Genes on the Same Chromosome are Linked biology are grounded in classical or Mendelian Genetics. 2.5.1. Meiosis: chromosomes assort independently Once the relationship between traits and genes was 2.5.2. Mapping genes on chromosomes understood, the relationship between cells and genetics 2.6. Quantitative Genetics: Traits that are Continuously Variable was investigated, leading to the discovery of 2.7. Population Genetics: Traits in groups of individuals chromosomes, and a quest for the substance that carried the genetic information began, culminating in the discovery of DNA. These studies constitute the contribution of classical genetics to the founding of the genomic era. CONCEPTS OF GENOMIC BIOLOGY Page 1 In 1859 Charles Darwin published his book On the (RETURN) Origin of Species. In this work Darwin described a mass of descriptive support for the concept that 2.1. MENDEL & DARWIN – “traits” are stably transmitted through subsequent TRAITS ARE CONDITIONDBY GENES. generations, and that organisms that have superior traits survive their natural environment to pass those The idea of genomic biology begins with a traits on to the next generation. However, Darwin did consideration of what makes up genomes. not describe any mechanism for such transmission of Specifically what are genes. The timeline of genetics traits to the next generation. and genomics begins with the early work of Charles Experimental evidence for a mechanism explaining Darwin and Gregor Mendel who didn’t really talk how traits pass to subsequent generations came in about genes per se, but who did describe the 1866 when an Austrian monk, Gregor Mendel, behavior of the characteristics of biological published his studies covering 10 years worth of work organisms, which they referred to as traits. on the mechanism of inheritance of 7 characteristics in garden peas in a paper called “Experiments in Plant Hybridization”. Charles Darwin Gregor Mendel CONCEPTS OF GENOMIC BIOLOGY Page 2 The law of independent segregation. Inherited characteristics (such as stem length in Mendel's pea plants) exist in alternative forms (tallness, shortness)—today known as alleles. For each characteristic, an individual possesses two paired alleles—one inherited from each parent. Correspondingly, these pairs segregate (i.e. separate or assort) in germ cells and recombine during reproduction so that each parent transmits one allele to each offspring. Mendel's Experiments Video The law of independent assortment. Specific traits In 1865 Mendel delivered two long lectures that operate independently of one another. A pea plant might have a stem that is tall or short, but in either were published in 1866 as "Experiments in Plant case may produce white or gray seed coats. Hybridization." This established what eventually became formalized as the Mendelian Laws of However, the significance of Mendel’s work and his inheritance: insight into the mechanism of inheritance went unrecognized until 1900 when three European The law of dominance. For each trait, one factor scientists, Hugo de Vries, Carl Correns, and Erich von (gene) is dominant and appears as the phenotype in Tschermak reached similar conclusions in their own the first filial generation (F1). In the F2 generation the dominant trait occurs more often, in a definite 3:1 research though they claimed to be unaware of ratio. The alternative form is recessive. In Mendel's Mendel’s earlier theory of the 'discrete units' on peas, tallness was dominant, shortness recessive. which genetic material resides. Therefore, three times as many plants were tall as The biological entity (factor) responsible for were short. This constant ratio represents the random defining traits was later termed a gene by Wilhelm combination of alleles during reproduction. Any Johansen in 1910, but the biological basis for combination of alleles that includes the dominant inheritance remained unknown until DNA was allele will express that form of the trait. identified as the genetic material in the 1940s. Thus, CONCEPTS OF GENOMIC BIOLOGY Page 3 it was early in the 20th century that the name “gene” American graduate student, in 1902 at about the same was given to the hereditary unity described by time that Mendel’s Laws of inheritance were being Mendel decades earlier, and the study of genetics and rediscovered. genomics began in earnest. The developing theory stated: (RETURN) More than one gene is located on each chromosome. 2.2. GENES ARE CARRIED ON CHROMOSOMES. Thus, chromosomes are like a string of beads with each gene represented as a bead. Along the length of At about the same time that genes were coming the chromosome (string of beads) there are genes for into focus as having a role in inheritance, a series of many traits on each chromosome, and each gene observations at the cellular level established: occupies a specific position on each chromosome The existence of structures called chromosomes. called a locus. The chromosomes are passed from one generation to the next and carry genes to the next generation as they are passed. These points were incorportated into what we now know as the Chromosomal Theory of Inheritance. (RETURN) Chromosomes carry genes. The notion that Mendel’s particulate hereditary factors reside on visible structures called chromo-somes was originally independently proposed by Theodor Boveri, a German scientist, and Walter Sutton, an CONCEPTS OF GENOMIC BIOLOGY Page 4 (RETURN) 2.3. THE CHROMOSOMAL THEORY OF INHERITANCE. In the early years of the 20th century Thomas Hunt Morgan, who was skeptical about the theories of the day concerning Mendel’s observations and the role of chromosomes in inheritance, began conducting a series of experiments using the fruit fly, Drosophilla melanogaster, that ultimately convinced him of the details of inheritance leading to what is called today Figure 2.1. The complete set of 23 pairs of human chromosomes is shown in the karyotype above. Note the chromosomal theory of inheritance. The general that there are 22 pairs of autosomal Chromosomes, and tenets of this theory are given below: the X and Y sex chromosome “pair”. Thus, we say that there are 22 pairs of homologous autosomal Multiple genes conditioning the cellular and chromosomes plus a pair of sex chromosomes (X or Y) organismal traits an organism possesses are passed in humans, and humans have 46 (diploid number) from one cellular or organismal generation to the next chromosomes in total. on chromosomes. Genes for specific traits reside at specific positions on chromosomes called loci (singular locus). The complete set of human chromosomes is shown in Figure 2.1. Humans have 22 pairs of autosomal Most cells of an organism have homologous pairs of chromosomes, and the X and Y sex chromosomes that chromosomes for each chromosome found in the cell. are present in males (XY) of females (XX). Thus, we say The complete set of chromosomes an organism that there are 22 pairs of homologous autosomal possesses is called it’s karyotype. chromosomes plus a pair of sex chromosomes (X or Y) in humans. Humans have 46 chromosomes in total, and the diploid number of chromosomes is 26. CONCEPTS OF GENOMIC BIOLOGY Page 5 Gametes, eukaryotic cells that pass chromosomes to the next organismal generation, contain only a haploid number of chromosomes (23 in the case of The genotype that an organism possesses in homans). Thus, gametes have only 1 chromosome combination with environmental factors is responsible from each pair found in a non-gametic cell. for production of the trait that we see. This is also a Chromosome numbers are constant for a species, but definition of the phenotype of an individual, i.e. the vary from one species to another. appearance of the individual resulting from the interaction of genotype and environmental factors. One of the chromosomes in each homologous pair Thus, an organism can demonstrate a dominant comes from the maternal parent while the other phenotype or a recessive phenotype. chromosome in the pair comes from the paternal parent. Although traits are conditioned by genes at specific What Mendel observed was the phenotype of his loci on the chromosomes, the gene at a given locus pea plants. From observations of phenotype he coming from each parent may not be the same. They proposed a model for genotypic behavior of his can be either the dominant (according to Mendel’s law “factors” that we no know as genes. We also know of dominance) factor, ort he recessive factor. We now that these genes reside on chromosomes, and the call the nature of the factor (gene) at each locus, an manner in which the chromosomes are passed to the allele. next generation provides the basis for Mendel’s law When both the maternal and paternal homologous of segregation that directly relates the behavior of the chromosome contain the same allele, the organism is chromosomes bearing the genes to the phenotypic said to be homozygous, but if the alleles contained at the locus on the homologous chromosomes are behavior that Mendel observed. However, there are different the organism is said to be heterozygous. a number of instances where, although Mendel’s law of segregation applies additional background is When an organism is homozygous, if the allele it bears is the dominant allele, the organism demonstrates a required to appreciate how such Mendel’s work homozygous dominant genotype.
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